Asked 7 years, 2 months ago. How can I merge and process multiple rows from a file to produce a report using perl Ask Question. Improving the question-asking experience. What do you want in the gene header record? Sign up or log in Sign up using Google.

To do the second thing you ask, capture the hi and lo values in your first pass, and store them. Sign up using Facebook.

I’ve modified this code following the 4th comment. Unicorn Meta Zoo 9: Email Required, but never shown. You might like to consider editing the original question rather than adding comments – it will be a lot easier to read and interpret.

To get value from the row of extracted region, i. I hope that’s sufficiently commented to make sense. And up-vote my answer. Sign up using Email and Password. Post as a guest Name. When I ran it with the sample data, I got no warnings, so perhaps the full data has inconsistencies not obvious from the sample.

By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. What do you want in the gene header record?

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Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. It’s hard to tell from your original sample.

What I’ve written is not complex code, it has comments and structure. I would suggest to you that you should “cure the cause, not the effect”.

I am new perl 55.6 tried with little messy code. Asked 7 years, 2 months ago. It’s time for you to come to grips with the logic of it. Just to reinforce that previous comment, no warnings ‘uninitialized’; is a very bad idea. If one sequence has a – will they all? It was written with perl5 in mind.

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Geeious first question is just a regexp, which I think you’ve got the general hang of. The program is telling you “something is geneikus here that is unexpected, or that you haven’t allowed for”. I am using perl 5 version, so added to the code: In nearly 20 years of writing perl, I’ve used that pragma only a handful of times, and only ever with the local scope of a code-block or sub, never as a global switch. If the oil light on your car’s dashboard comes on, would you check the oil, or just take the light-globe out?

There’s an assumption that all sequences for a gene have the same direction. It’s the same principle. It looks like what you’re trying to achieve is to merge the details from the line labelled CDS with the matching line labelled extracted regionand then print the merged results with a leading summary header, based on some minimum and maximum values, grouped by Name.

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